if it has a standard clutch and is running 1.0 bar.. it will eventually chew the clutch.. but your not sure what clutch is in there. when my clutch was on the way out, it made shifting difficult, most just slip.
sometimes changing the transmission oil can sort out dodgy noises when shifting.. some people reccomend redline mt90 gear oil as it's pretty good.
beyond that, one of the more techy people on here may be able to help diagnose the noise (like a nut in a can).. start asking questions about synchro on first, selector forks, and that kind of thing and see where it gets you.
sorry i can't be any more help mate. i know its worrying to have un diagnosed gearbox issues. and your thinking, how big is the bill going to be?????? erk

somone one will point you in the right direction